Experimental Oncology

6 EC

Semester 1, period 1

5234EXPO6Y

Owner Master Biomedical Sciences
Coordinator prof. dr. R.L. Beijersbergen PhD
Part of Master Biomedical Sciences, track Oncology,

Course manual 2025/2026

Course content

The master course experimental oncology deals with the main themes of basic cancer research and treatment, the implications of groundbreaking new research for diagnosis and treatment of cancer, and the clinical implementation. Teachers are fundamental researchers and clinicians involved in the development and implementation of state-of-the-art cancer therapies. Topics include e.g. molecular cancer diagnostics, the hallmarks of cancer, mechanisms of drug resistance, immunotherapy of cancer. The course evolves around four major themes; hormone regulated cancers, DNA damage and genomic instability, targeted therapy and resistance and immunology and immunotherapy. Lectures covering different fields of research and treatment provide background and reference.  The different topics will be dealt with in lectures, workshops and assignments (essay with pitch presentation,  a group assignment with presentation and a research proposal with pitch).

Recommended  prior knowledge
Solid, advanced knowledge in the areas of cell biology and genetics (eg. courses Celbiologie (6 EC), Moleculaire Biologie/Biochemie (T) (6 EC), Anatomie en Ontwikkelingsbiologie (12 EC), Medische Biochemie en Pathofysiologie (12 EC)).

Study materials

Literature

  • The biology of cancer by R.A. Weinberg (2nd edition). 

Syllabus

  • electronic copies of Handouts

Objectives

  • Aim of the course Experimental Oncology is to provide insight into the molecular basis of normal and tumor cell behaviour 
  • to provide insight into the development of new methods for cancer diagnosis and therapy.
  • To review and discuss the historical context and evidence for novel targeted cancer therapies
  • To review, analyse and discuss the up-to-date status of the field in relation to an outstanding research question in oncology
  • The ability to create and present a research proposal related to subject in the filed of oncology

Teaching methods

  • Lecture
  • Presentation/symposium
  • Self-study
  • wiring a research proposal
  • Supervision/feedback meeting
  • Working independently on e.g. a project or thesis
  • Computer lab session/practical training

Lectures provide the general background and the current standing of the respective clinical or research field. They also introduce the latest developments and insights in the respective research area. lectures given by experts in the respective research field.

There will be 4 workshops each around a specific theme. Students will get assignments which will be discussed within the group.

There will be introductions for the assignments and a workshop "how to write a research proposal.

There are 4 "interview the teacher" sessions in which the students prepare questions based on information provided by the teacher to get familiar with the research field, the current concepts and discuss open questions. 

The students have to write a short essay on the historical development of a targeted drug in clinical use (assignment 1)

The student have to create a research portfolio which forms the basis of the research proposal that has to be written in the last week of the course (assignment 2). There will be different time-pint at which dates on the portfolio need to be submitted.

The students have to address an outstanding question in oncology in a small group. They have to investigate recent findings, implications, shortcomings and future research for this question in relation to technological developments. The group presents the findings  in a presentation (assignment 3).

Each student has to independently write a research proposal on a research topic  captured during the course. They will have to define the research question and discuss its relevance, generate a hypothesis, discuss the experimental approach to test the hypothesis and discuss the potential outcomes. Each student will present the research proposal in a pitch presentation followed by a short discussion (assignment 4). 

During the course introductions and workshops are provided for the different assignments in the course. The students will provide feedback to their peers and will receive feedback on the different steps in the assignments. There will be three days in which different assignments in small groups will be completed and presented to the group. One workshop will be aimed at large-data mining in oncology with the help of on-line analysis tools concluded with a assignment (assignment 5). 

 

Learning activities

Activity

Number of hours
lectures 30
workshops 36
preparation 42
presentations 15
feedback 8
Self Study 27
 Totaal 6 EC a 28 h 168

 

Attendance

  • Some course components require compulsory attendance. If compulsory attendance applies, this will be indicated in the Course Catalogue which can be consulted via the UvA-website. The rationale for and implementation of this compulsory attendance may vary per course and, if applicable, is included in the Course Manual.

    • Additional requirements for this course:

    presence at lectures and  workshops  is mandatory

    Completion of assignments, written and presentations is mandatory

    Absence needs to be communicated with the course coordinator

    Assessment

    Item and weight Details

    Final grade

    10%

    assignment 1 drug assay

    		Must be ≥ 5.5

    10%

    assignment 2 research portfolio

    		Must be ≥ 5.5

    25%

    assignment 3 outstanding problem

    		Must be ≥ 5.5

    40%

    assignment 4 research proposal

    		Must be ≥ 5.5

    5%

    assignment 5 data analysis

    		Must be ≥ 5.5

    The final grade is the average of  assignment 1 (10%), assignment 2 (10%)  assignment 3 (25%), assignment 4 (40%), assignment 5 (5%). The scores for peer review of assignment 1 are bonus points adding 0.25 point (0 to 2 bonus points possible)

    For each assignment a score higher than 5.5 is needed to pass the course 

    The final grade has to be higher than a 5.5 to pass the course. 

    If a deadline for an assignment is not met, that part will  be graded zero ( 0)

     

     

    Inspection of assessed work

    Contact the course coordinator to make an appointment for inspection.

    The students can only request an appointment for inspection after all the grades are in and the final score has been calculated and communicated with the students.

    Assignments

    assignment 1 individual

    • exercise in writing a short essay about the history and development of a target therapeutic

      Peer review of short essay

       

    assignment 2 individual

    • research portfolio

    assignment 3 group

    • presentation about an outstanding question in oncology related to new technologies 

    assignment 4 individual

    • written research proposal on oncology related subject/problem

    assignment 5 individual

    • practical assignment

    Fraud and plagiarism

    The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

    Course structure

    Course Experimental Oncology 2025      
    Date   Sept 29 to October 24 2025  
    Location   room Z4 in NKI   
    WEEK 1      
    DATE / TIME   SUBJECT TEACHER
    MONDAY  29/Sep    
    9.30 - 10.00   START COURSE-pick up acces pass and coffee/tea in room Z4
    10.00 - 10.50   Introduction assignment 1 Roderick Beijersbergen
    coffee break      
    11.10 - 12.00   Advanced early cancer diagnostics Beatriz Carvalho
    12.10 - 13.00   Advanced early cancer diagnostics Beatriz Carvalho
           
        Self-study preparation lecture Clinical trials 30/9 paper @ Surfdrive
    TUESDAY 30/Sep    
    9.00 - 9.50   Clinical trials  - Masterclass - read paper first Marcel Soesan
    10.00 - 10.50   Clinical trials  - Masterclass Marcel Soesan
    coffee break      
    11.10 - 12.00   Epidemiology of cancer  Marjanka Schmidt
    12.10 - 13.00   Epidemiology of cancer Marjanka Schmidt
           
        preparation assigment 1  
    WEDNESDAY 1/Oct    
    9.00 - 9.50   Workshop  Hormone Regulated Cancers Willbert Zwart
    10.00 - 10.50     Hugo Horlings
    coffee break      
    11.10 - 12.00   Tour @ Pathology department - 2 groups Maarten Breet
    12.10 - 13.00     Andre Bergman
    lunch break      
    13.30 - 16.00 Z1? feedback and discussion assigment 1 Roderick Beijersbergen
    THURSDAY 2/Oct    
    9.00 - 9.50   assignment 2 Roderick Beijersbergen
    10.00 - 10.50      
    coffee break      
    11.10 - 12.00   assignment 2  
    12.10 - 13.00      
    lunch break      
    13.30 - 14.20   assignment 2  
    14.30 - 15.20      
    FRIDAY 3/Oct    
    9.00 - 9.50   assignment 2 Roderick Beijersbergen
    10.00 - 10.50      
    coffee break      
    11.10 - 12.00   assignment 2  
    12.10 - 13.00      
    lunch break      
    13.30 - 14.20   assignment 2  
    14.30 - 15.20      
           
    WEEK 2      
    DATE / TIME   SUBJECT TEACHER
    MONDAY  6/Oct    
    9.00 - 9.50   Next generation sequencing Arno Velds
    10.00 - 10.50   Next generation sequencing Roderick Beijersbergen
    coffee break      
    11.10 - 12.00   Introduction assignment 3 Roderick Beijersbergen
    12.10 - 13.00   Introduction research proposal Roderick Beijersbergen
    lunch break      
    13.30 - 15.00   preparation assigment 3 in groups
        Preparation interview the teacher: Benjamin Rowland  
           
    TUESDAY 7/Oct    
    9.00 - 9.50   DNA damage tolerance Heinz Jacobs
    10.00 - 10.50   DNA damage tolerance Heinz Jacobs
    coffee break      
    11.10 - 12.00   Interview the teacher:  Benjamin Rowland
    12.10 - 13.00   Shaping the genome in interphase and mitosis  
           
    WEDNESDAY 8/Oct    
    9.00 - 9.50   Workshop  Epigenetics and Cancer  
    10.00 - 10.50     Elzo de Wit
    coffee break     Fred van Leeuwen
    11.10 - 12.00      
    12.10 - 13.00      
    lunch break      
    13.30 - 14.20   How to write a research proposal Roderick Beijersbergen
    14.30 - 15.20   How to write a research proposal Roderick Beijersbergen
           
    THURSDAY 9/Oct    
    9.00 - 9.50   mRNA translation and Reuven Agami
    10.00 - 10.50   cancer immunotherapy Reuven Agami 
    coffee break      
    11.10 - 12.00 kan Telomeres, DNA damage and cancer Jacqueline Jacobs
    12.10 - 13.00 kan Telomeres DNA damage and Cancer Jacqueline Jacobs
    lunch break      
    13.30 - 15.00   feedback and discussion assigment 3 Roderick Beijersbergen
           
    FRIDAY 10/Oct    
        preparation assignment 3 and research proposal @ home  
           
    WEEK 3      
    DATE / TIME   SUBJECT TEACHER
    MONDAY  13/Oct    
    9.00 - 9.50   Cancer genomics Lodewyk Wessels
    10.00 - 10.50   Cancer genomics Lodewyk Wessels
    coffee break      
    11.10 - 12.00   AI for Oncology Jonas Teuwen
    12.10 - 13.00   AI for Oncology Joren Brunekreef-Postdoc T.group
    lunch break      
    13.30 - 15.00   preparation assignment 3 and res. proposal in groups
        preparation Interview Rene Bernards  
    TUESDAY 14/Oct    
    9.00 - 9.50   Targeted Therapy Roderick Beijersbergen
    10.00 - 10.50   Targeted Therapy Roderick Beijersbergen
    coffee break      
    11.10 - 12.00   Interview the teacher: Rene Bernards
    12.10 - 13.00   Novel strategies for targeted therapy  Rene Bernards
    lunch break      
    13.30 - 15.00   preparation assignment 3 in groups
        and research proposal  
           
    WEDNESDAY 15/Oct    
    9.00 - 9.50   Workshop: Functional genomic screening  
    10.00 - 10.50     Abdel Mazouzi
    coffee break     Roderick Beijersbergen
    11.10 - 12.00     Johan Kuiken
    12.10 - 13.00      
        preparation Interview Jacco van Rheenen/Mark de Gooijer 16/10  
        preparation assignment 3 and research proposal  
           
    THURSDAY 16/Oct    
    9.00 - 9.50   Protein structure and drug design Titia Sixma
    10.00 - 10.50   Protein structure and drug design Titia Sixma
    coffee break      
    11.10 - 12.00   title Hendrik Messal
    12.10 - 13.00   Interview the teacher Cancer Stem cells Jacco van Rheenen
    lunch break      
    13.30 - 15.00   preparation assignment 3 in groups
        and research proposal  
           
    FRIDAY 17/Oct    
    9.00 - 9.50   presentations assignment 3 Roderick Beijersbergen
    10.00 - 10.50      
    coffee break      
    11.10 - 12.00   presentations assignment 3  
    12.10 - 13.00      
    lunch break      
    13.30 - 14.20   presentations assignment 3  
    14.30 - 15.20      
           
    Week 4      
    DATE / TIME   SUBJECT TEACHER
    MONDAY  20/Oct    
    9.00-9.50   assignment 4 Roderick Beijersbergen
    10.00-10.50      
    coffee break      
    11.10 - 12.00   assignment 4  
    12.10 - 13.00      
    lunch break      
    13.30 - 14.20   assignment 4  
    14.30 - 15.20      
        preparation Interview Daniel Peeper  
           
    TUESDAY 21/Oct    
    9.00-9.50   The study of mouse models for cancer Jos Jonkers/Stefan Hutten
    10.00-10.50   The study of mouse models for cancer Jos Jonkers
    coffee break      
    11.10 - 12.00   Interview the teacher:  Daniel Peeper
    12.10 - 13.00   Cancer immune surveillance: concepts,  Daniel Peeper
        challenges & opportunities  
           
        preparation research proposal  
           
    WEDNESDAY 22/Oct    
    9.00 - 9.50   Workshop: Immunotherapy  
    10.00 - 10.50     Leila Akari group
    coffee break      
    11.10 - 12.00      
    12.10 - 13.00      
           
        preparation research proposal  
    THURSDAY 23/Oct    
    9.00 - 9.50   T-cell therapy Wouter Scheper
    10.00 - 10.50   TCR and Neoantigens Marius Messemaker
    coffee break      
    11.10 - 12.00   TBA Roderick Beijersbergen
    12.10 - 13.00   TBA Roderick Beijersbergen
           
        preparation research proposal and pitch presentation  
    FRIDAY 24/Oct    
    9.00 - 9.50   proposal pitches Roderick Beijersbergen
    10.00 - 10.50      
    coffee break      
    11.10 - 12.00   proposal pitches  
    12.10 - 13.00      
    lunch break      
    13.30 - 14.20   proposal pitches  
    14.30 - 15.20      
    15.30 - 16.30   Evaluation and Borrel  
           
    Sunday  24.00 26-Oct deadline research proposal  

    Additional information

    Course will be held at the NKI-AVL, Plesmanlaan 121, Amsterdam
    For information, contact mw. Patty Lagerweij (p.lagerweij@nki.nl)

    Homepage NKI-AVL: http://www.nki.nl

    Contact information

    Coordinator

    • prof. dr. R.L. Beijersbergen PhD